Human bacteria sequencing project involving CU raises $340,000 online

In hopes of better understanding nutrition and health, the University of Colorado Boulder is playing the leading science role in a “crowdfunding” effort that has raised more than $340,000 for a project designed to sequence the gut bacteria of thousands of people around the world.

Known as the American Gut project, the effort raised the money through a crowdfunding effort online in which collective groups of people pool money to support various initiatives, said CU-Boulder Associate Professor Rob Knight of the BioFrontiers Institute. The $340,477 raised for the American Gut project is the largest amount of money ever raised through crowdfunding for a science project, said Knight, who is co-leading the effort with Jeff Leach, founder of the Human Food Project.

The money contributed by 2,005 funders will be used to sequence gut bacteria from about 3,500 people said Knight. Each human is believed to harbor roughly 10 trillion microorganisms -- about 10 times more than the number of cells in the human body -- that undertake a number of important functions ranging from digesting food to the strengthening of immune systems.

In 2009, a consortium of 200 researchers from 80 institutions organized by the National Institutes of Health, including Knight, mapped the normal microbial makeup of healthy humans as part of the $173 million Human Microbiome Project. Building on the massive NIH effort, the American Gut project will be an “open source” effort, meaning participants will have access to the data gathered to help understand how diet and lifestyle may contribute to human health through the interaction of our microbiomes, cells and genes, said Knight.

“The outpouring of public support for this research project demonstrates how public awareness of the role of our microbial systems in human health is growing,” said Knight, the project’s scientific lead who holds joint faculty appointments in CU-Boulder’s chemistry and biochemistry department and computer science department. “By looking at samples from the general public, we can get a far better sense of what a ‘normal’ microbiome is and what factors have the largest effects.”

The scientists are particularly interested in how diet and lifestyle, whether by choice or necessity, affect peoples’ microbial makeup, including those suffering from particular autoimmune diseases or who have food allergies, said Knight, also a Howard Hughes Medical Institute Early Career Scientist.

“The large number of participants in American Gut, coupled with our ongoing work in Africa and South America, will allow us to explore the impact of diet and lifestyle between western and more traditional societies,” said Leach. “We may find that our modern gut microbiome has shifted significantly away from our ancestral one, but reinstating some of that primal balance may be within our grasp.”

“I’m super excited about helping to build a system that not only integrates so much data but also presents it to the user in a useful way,” said Meg Pirrung, a graduate student in Knight’s lab. “This is an amazing opportunity for me and everyone involved.”

Daniel McDonald, a graduate student in the BioFrontiers Institute’s IQ Biology Program, said the American Gut project is allowing him to hone his interdisciplinary experience. IQ Biology students are involved in semester-long rotations that immerse them in disciplines ranging from mathematical and computational biology to biophysics and bio-imaging. “It’s an extraordinary opportunity for discovery,” he said.

The American Gut data also will also be used in the several IQ Biology Program courses taught by Knight with Manuel Lladser, an associate professor in the applied mathematics department. Last year the IQ Biology program at CU’s BioFrontiers Institute, which offers doctorates in eight disciplines, was awarded a $3 million grant from the National Science Foundation’s Integrative Graduate Education and Research Traineeship, or IGERT.

Second Genome, a biotech company headquartered in San Bruno, Calif., is working with the American Gut project to explore the connection between the human microbiome and type 2 diabetes, said company president and CEO Peter DiLaura.

“The American Gut project has succeeded in bringing together the largest citizen science network ever for human microbiome sample collection,” DiLaura said. “By building this extensive reference database, we now have the opportunity to explore the connections between the human microbiome and metabolic and inflammatory diseases.”

Although the first round of funding that enabled the project to commence has ended, a second phase also allows anyone in the world to join, said Leach. Once the scientific results are in from the initial group of participants, a third phase will allow new participants to obtain additional analyses crucial to understanding the microbiome.

“By integrating the tens of thousands of environmental samples that the scientific community has provided from around the world and applying powerful modeling approaches, we will be able to gain unprecedented insight into the links between our own microbes and those in our environment,” said Argonne National Laboratories microbial ecologist Jack Gilbert, a member of the Earth Microbiome Steering Committee.

“With advances in DNA sequencing, we are moving towards a world in which no infectious disease goes undiagnosed, and in which we have full knowledge of the microbes that inhabit us and our surroundings,” said Knight. “By participating in this project, thousands of people are helping us to make this future a reality.”

Quotes

“The outpouring of public support for this research project demonstrates how public awareness of the role of our microbial systems in human health is growing,” said Rob Knight, the project’s scientific lead who holds joint faculty appointments in CU-Boulder’s chemistry and biochemistry department and computer science department. “By looking at samples from the general public, we can get a far better sense of what a ‘normal’ microbiome is and what factors have the largest effects.”